Course Information

HST 583- Functional Magnetic Resonance Imaging: Data Acquisition and Analysis (H)

Suggested Background Courses: Linear Algebra (18.06, e.g.) and Differential Equations (18.03, e.g.). Introductory or college level courses in neurobiology (9.01, e.g.), physiology, probability (6.041, e.g.), and physics (8.01 and 8.02, e.g.) are preferred. See Dr. Gollub to determine if course is right for you.

Fall Semester 2006: (2-2-8) units.

Monday lectures 3:00-4:00 PM and Wednesday lectures 3:00-4:00 PM, Monday laboratory 1:00 to 2:30 PM and Wednesday discussion section 2:00 to 3:00 PM.

Lecture and discussion will be held at E25-119 and labs at 1-115 or 26-139 (unless otherwise noted).
The majority of the computer labs will be run using Neurolens fMRI Analysis Software, Slicer Software, and Matlab (see resources page)

First class: Wednesday Sept. 6th, 3 PM. (See course web site for further updates).

Format: Monday/Wednesday 60-minute lectures and weekly laboratory and discussion sessions. Laboratory will include fMRI data acquisition sessions and data analysis workshops. Assignments include reading of the primary textbook chapters and primary literature as well as fMRI data analysis in the laboratory.

This team taught, multidisciplinary course covers the fundamentals of magnetic resonance imaging relevant to the conduct and interpretation of human brain mapping studies. The challenges inherent in advancing our knowledge about brain function using fMRI are presented first to put the work in context. The course then provides in depth coverage of the physics of image formation, mechanisms of image contrast, and the physiological basis for image signals. Parenchymal and cerebrovascular neuroanatomy and application of sophisticated structural analysis algorithms for segmentation and registration of functional data are discussed. Additional topics include fMRI experimental design including block design, event related and exploratory data analysis methods, building and applying statistical models for fMRI data. Human subjects issues including informed consent, institutional review board requirements and safety in the high field environment are presented.

Course Director: Randy Gollub (
Instructors:B. Rosen, L. Wald, B. Dickerson, K. Helmer, R. Banzett, J. R. Melcher, R. Savoy, D. Salat, D. Kennedy, M. Vangel, D. Greve, A. Yendiki, J. Mandeville, D. Sodickson, S. Pujol, R. Buckner, N. Hadjikhani, V. Napadow, S. Gabrieli, J. Gabrieli, C. Triantafyllou